1- I don't think so, the surprise effect is still there if the brat activates the relay, no one is going to oppose any serious resistance to such an invasion. Furthermore he would control the whole relay transmissions. Also after the harvest no one is going to tell what happened there. And it's much preferable to activate the Citadel than losing three years and giving the opportunity to the galaxy races to prepare themselves for the war. As for the brat creating the Reapers but being unable to control the Citadel which was built by the Reapers? Yeah, no. The keepers are doing "physical" maintenace, something he as dematerialized entity can't do.
You know, I've hanging around here for a while and I can't remember how much threads were made to explain the plot hole, retcon, problem created by the brat's presence on the Citadel. Trying to explain it is left to speculation.
But the signal to activate the Citadel as a relay did not work at that point, so it implies to me the Catalyst can't do jack about that. So how could it interfere? Revealing itself at that point doesn't make any sense if it can't interfere anyway. Reapers still wouldn't be able to come through the relay, but Citadel inhabitants might get wind of it and get suspicious.
Yup, that's their main purpose, but more importantly the Keepers are also the ones responding to the Reaper signal and activating the relay. If the Catalyst could do that, why would it need the Keepers to take care of it? It probably gave them this task a long time ago, but even so, seems to me it is not responsible for the signal.
But yeah, a lot of it is speculation, so... we could stop if you want 
2- That wasn't the point. The brat tries hard to explain to me that the Reapers are actually the good guys who seek to preserve life (in whatever form) and prevent the organics races to be wiped by evil robots we've created.The Rachni almost disappeared because the Reapers brainwashed them and pushed them to war. You can even seal their destiny by killing the last Queen. So my question is where is this so called preservation?
You're right that this isn't preservation at this point, but they could still be harvested after using them as enslaved species.
Or it simply has to do with rachni becoming a threat, so they use them as indoctrinated agents instead.
It was like that at least during the Sanctuary mission. They let Cerberus do a lot of things, but as soon as they found a way to actually control Reaper forces, they needed to be taken care of.
On a side note, you're using good and evil too much. It's not as black and white, and I think a lot of what the Catalyst says is based on its programming, and a rather neutral, observing approach. It simply states that Synthetics must by definition surpass their creators in order to become even more efficient to their needs. Is it not right about that? Once something is achieved, organics strife for more, for better. I actually think it is quite accurate with this statement.
5- I know about that Codex entry, it's only proving my point. The Reapers completely threw the most advanced race of the cycle in trash can by rewriting them genetically and use them as canon fodder. So even by the brats standards this is no preservation.
While that might be true, we don't know for sure why it didn't work out, or what really prevented them to store them in Reaper form. Something must have happened that they didn't go through with it.
6- On one hand the bratalyst is talking about how cool he and his pals are and how much they do care about life by ascending them in to Reaper form. Then he sends those very ships to war risking the complete disappearance of what he "preserved". How logic is that? How much ships the Reapers did losein this war, how much civilizations just simply ceased to exist?
It never talked about how "cool" it is. Where did you get that?
He sends them to war because it sees it as a perfected way to do so. And it was right so far, wasn't it? Creating the Citadel as a trap worked for countless cycles, only now it's different, and only because the Protheans were able to change one little thing in their chain reaction, or else the current cycle would've fallen prey to the Reapers as well.
You said it yourself, how much ships the Reapers lost in this war. And that's the point. It's just different this time, it never met that kind of resistance before, a whole galaxy united.
3- Saren was in Sovereign's palm. Why go to the Geth in the first place? Why push them to war? To self fullfill the brat's prophecy? Same goes for the Metacons. And even then not all the Geth were for a war with the organics. In fact just a small faction of them. So how much credit should I give to the brat's babble? Don't forget he's enouncing absolute, immuable laws on which he based his whole final solution.
7- Right but enough to disprove his logic based on absolute assumptions...
According to Legion it was still the geth's own wish to intervene? "made their own decision" sounds to me they wanted this, wanted to serve "the old machine". It is also too late at this point to say it only now fullfilled the prophecy, they fullfilled the prophecy as soon as they rebelled against the quarians.
You say that not all geth wanted the war. But still they fight to "survive" if need be. They would turn on organics again and again if their existence is threatened, as seen when you refuse Legion to let it upload the Reaper code on Rannoch.
I mean, I get it, you don't like the Catalyst and that's fine. But if it witnessed something, say 100000 times, and one or two times it happened differently, do you really think that counts for something? It is not really an assumption, but the fact it saw it happening for the 100000 times slighty outnumbers the other occurences, imo.